PDBsum entry 5o6t

Ligase

PDB id: 5o6t

Contents

Protein chains

64 a.a.

75 a.a.

Ligands

EDO ×2

Metals

_ZN ×4

Waters ×218

PDB id:

5o6t

Name:

Ligase

Title:

Birc4 ring in complex with dimeric ubiquitin variant

Structure:

E3 ubiquitin-protein ligase xiap. Chain: a, b. Synonym: baculoviral iap repeat-containing protein 4,iap-like protein,hilp,inhibitor of apoptosis protein 3,hiap3,ring-type e3 ubiquitin transferase xiap,x-linked inhibitor of apoptosis protein,x- linked iap. Engineered: yes. Polyubiquitin-b. Chain: c, d.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: xiap, api3, birc4, iap3. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Gene: ubb. Expression_system_taxid: 469008

Resolution:

1.57Å R-factor: 0.158 R-free: 0.183

Authors:

M.Gabrielsen,L.Buetow,D.T.Huang

Key ref:

M.Gabrielsen et al. (2017). A General Strategy for Discovery of Inhibitors and Activators of RING and U-box E3 Ligases with Ubiquitin Variants. Mol Cell, 68, 456. PubMed id: 29053960

Date:

07-Jun-17 Release date: 01-Nov-17

Protein chains

P98170  (XIAP_HUMAN) -  E3 ubiquitin-protein ligase XIAP from Homo sapiens

Seq: 497 a.a.

Struc: 64 a.a.

Protein chains

P0CG47  (UBB_HUMAN) -  Polyubiquitin-B from Homo sapiens

Seq: 229 a.a.

Struc: 75 a.a.*

* PDB and UniProt seqs differ at 16 residue positions (black crosses)

Enzyme reactions

• Enzyme class 2: Chains A, B: E.C.2.3.2.27 - RING-type E3 ubiquitin transferase.
• Reaction: S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N₆- ubiquitinyl-[acceptor protein]-L-lysine
• Enzyme class 3: Chains C, D: E.C.?

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Mol Cell 68:456 (2017)

PubMed id: 29053960

A General Strategy for Discovery of Inhibitors and Activators of RING and U-box E3 Ligases with Ubiquitin Variants.

M.Gabrielsen, L.Buetow, M.A.Nakasone, S.F.Ahmed, G.J.Sibbet, B.O.Smith, W.Zhang, S.S.Sidhu, D.T.Huang.

ABSTRACT

RING and U-box E3 ubiquitin ligases regulate diverse eukaryotic processes and have been implicated in numerous diseases, but targeting these enzymes remains a major challenge. We report the development of three ubiquitin variants (UbVs), each binding selectively to the RING or U-box domain of a distinct E3 ligase: monomeric UBE4B, phosphorylated active CBL, or dimeric XIAP. Structural and biochemical analyses revealed that UbVs specifically inhibited the activity of UBE4B or phosphorylated CBL by blocking the E2∼Ub binding site. Surprisingly, the UbV selective for dimeric XIAP formed a dimer to stimulate E3 activity by stabilizing the closed E2∼Ub conformation. We further verified the inhibitory and stimulatory functions of UbVs in cells. Our work provides a general strategy to inhibit or activate RING/U-box E3 ligases and provides a resource for the research community to modulate these enzymes.